(needs Cytoscape)

(needs Cytoscape)

(needs Cytoscape)








How To

Create a reaction with the following syntax:
ComponentA_[Domain/Subdomain(Residue)]_reaction_ComponentB_[Domain/Subdomain(Residue)]
Domain, Subdomain, and Residue are optional
ComponentA_reaction_ComponentB
Contingencies (constraints under which a reaction occur) can be define on the same line as the reaction and are separated by ;
Contingencies consist of a contingency symbol and a state separated by a space.
A_ppi_B
A_ppi_C; ! A--B 
Boolean contingencies can be chained as follows
A_ppi_C
A_ppi_D
A_P+_B; ! <mybool>
<mybool>; OR A--C; OR A--D
Inputs and Outputs can be defined as contingencies by using square brackets.
Input:
A_P+_B; ! [high_pH]
Output:
[RESPONSE]; ! B-{P}
For relocalisation reactions that move more than one molecule you need to add the molecules you want to be relocalized in a comma seperated list
A_SymExtCyt_B,C
            
Relocalisation reaction that need more than one molecule are:
  • SymExtCyt
  • SymCytVac
  • SymCytMit
  • SymCytEnd
  • APExtCyt
  • APCytVac
  • APCytMit
  • APCytEnd


Available Contingency Symbols

Symbol Description
! Absolutely required
K+ Positive effector
0 No effect
K- Negative effector
x Absolutely inhibitory
? Unknown
AND Used when several states are required for a certain effect (Intersection of states)
OR Used when several states can give an effect individually (Union of states)

Available Reaction Types

(Genetic evidence only (g_) or mapped from review paper (r_):)

SymbolNameReversibility
P+phosphorylationirreversible
P-dephosphorylationirreversible
APAutophosphorylationirreversible
PTPhosphotransferreversible
GEFGuanine Nucleotide Exchangeirreversible
GAPGTPase Activationirreversible
Ub+Ubiquitinationirreversible
CUTProteolytic cleaveageirreversible
ppiprotein-protein interactionreversible
ipiintra-protein interactionreversible
iinteraction (non-proteins)reversible
BINDBinding to DNAreversible
TRSCTranscriptionirreversible
TRSLTranslationirreversible
DEGDegradationirreversible
NIMPNuclear importirreversible
NEXPNuclear exportirreversible
MIMPMitochondrial importirreversible
MEXPMitochondrial exportirreversible
TrnsCytExtPlasma membrane Cyt-˃Ext ATPase pumpirreversible
TrnsCytVacVacuolar Cyt-˃Vac ATPase pumpirreversible
SymExtCytPlasma membrane symporterreversible
SymCytVacVacuolar membrane symporterreversible
SymCytMitMitochondrial membrane symporterreversible
SymCytEndEndosomal membrane symporterreversible
APExtCytPlasma membrane antiporterirreversible
APCytVacVacuolar membrane antiporterirreversible
APCytMitMitochondrial membrane antiporterirreversible
APCytEndEndosomal membrane antiporterirreversible
FDExtCytPlasma membrane channelreversible
FDCytVacVacuolar membrane channelreversible
FDCytMitMitochondrial membrane channelreversible
FDCytEndEndosomal membrane channelreversible

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